Re: [Freesurfer] [WARNING: UNSCANNABLE EXTRACTION FAILED]Re: [WARNING: UNSCANNABLE EXTRACTION FAILED]talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED***

page-up/page-down or the arrow keys should scroll through slices. Or alt-[xyz] to change the viewing orientation On Thu, 28 Mar 2019, Chhavi Yadav wrote: External Email - Use Caution Hi all,So after recon-all -autorecon1 -i slicename, I got a volume brainmask.mgz.  When I op

Re: [Freesurfer] [WARNING: UNSCANNABLE EXTRACTION FAILED]Re: [WARNING: UNSCANNABLE EXTRACTION FAILED]talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED***

External Email - Use Caution Hi all, So after recon-all -autorecon1 -i slicename, I got a volume brainmask.mgz. When I open brainmask.mgz in freeview, I can only see one output slice corresponding to the input slice. How do I see all the other slices or the volume? On Mon, Mar 25,

[Freesurfer] Group X Time Interaction in Qdec

External Email - Use Caution *What is the best way to run a whole- brain Group (intervention group, control group) x Time (Pre, post) interaction via QDEC? (https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/QdecGroupAnalysis_freeview

Re: [Freesurfer] regions of Yeo 17 networks in fast

External Email - Use CautionThanks!By these command lines the analysis are going fine.mri_surf2surf --srcsubject fsaverage5 --trgsubject subj --hemi rh --sval-annot /Applications/freesurfer/1000subjects_reference/Yeo_JNeurophysiol11_SplitLabels/fsaverage5/label/rh.Yeo2011_17Network

Re: [Freesurfer] nu_correct: Command not found

Hi Ian, I think I've seen something like this before, and I remember it relating to how FS was sourced. Are you setting FREESURFER_HOME before or after you source SetUpFreeSurfer.sh? And after you source FS, what's the output of `echo $MNI_DIR`? best, Andrew On 3/28/19, 11:02 AM, "freesurfer

[Freesurfer] nu_correct: Command not found

External Email - Use Caution Hello all. I am attempting to run recon-all in a docker container.  I have a set of commands to set up the system, and on my local machine (Ubuntu) it works fine.  However on the docker container (also Ubuntu) I get nu_correct: Command not found. I

Re: [Freesurfer] Special image protocol

hard to say without seeing all the parameters (which look like they were cropped out). It does seem correct. If you acquire one and send it to me I'll take a look. Probably best to send it directly to me, not on list though cheers Bruce On Thu, 28 Mar 2019, Mustafa Amin wrote: >Exter

Re: [Freesurfer] Protocol for MRI

External Email - Use Caution Hi, attached a 1mm MPRAGE Protocol for Philips 3T ~ 5min. You need a 3D TFL sequence with inversion pulse and fat satturation. Best, Joerg >     External Email - Use Caution    > > Hi Bruce/ Doug, > > This is the picture I got from the MRI o

[Freesurfer] tract all prep error mv: cannot stat ?/project/3015068.01/sub030/dmri/dwi_orig_las.nii.gz?: No such file or directory

External Email - Use Caution Hallo, I wrote to the mailing list last Monday because after running tract-all prep I got the following error: segmentation fault (core dumped). I tried to run tract-all prep with more gb (50 gb). Now, I do not get anymore the tract-all.e file conta

[Freesurfer] Protocol for MRI

External Email - Use Caution Hi Bruce/ Doug, This is the picture I got from the MRI operator. She needed to know that she had done the right thing about the MP-RAGE sequence. Is this the right protocol? Please share some thoughts. Thank you for your kind attention and cooperati

Re: [Freesurfer] Special image protocol

External Email - Use Caution Hi Bruce, The MRI operator gave me this picture she needs to know whether we are on the right track. Is this the correct protocol? Thank you in advance. Yours faithfully, Mustafa M. Amin Department of Psychiatry Faculty of Medicine University of Sum